Contacts of the helix formed by residues 237 - 258 (chain B) in PDB entry 3W7F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.9 20.9 - - + -
33B GLN* 4.2 4.9 - - - +
145B LEU* 3.7 26.5 - - + +
233B PHE* 4.6 0.2 - - + -
234B SER* 3.0 21.9 + - - +
236B GLU* 1.3 78.8 - - - +
238B GLN* 1.3 55.6 + - - +
239B PRO 3.4 1.3 - - - -
240B ILE* 3.0 5.0 + - - +
241B ILE* 2.8 40.5 + - + +
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Residues in contact with GLN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ILE* 3.4 38.4 - - + +
231B LYS* 3.8 21.6 + - - +
233B PHE* 3.0 23.5 + - + +
234B SER 3.1 8.7 + - - +
235B ILE* 3.8 26.2 - - - +
237B ALA* 1.3 75.3 - - - +
239B PRO* 1.3 70.6 - - + +
241B ILE* 3.3 4.4 + - - +
242B GLU* 3.0 24.8 + - - +
284B TYR* 3.3 30.4 + - + +
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Residues in contact with PRO 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE 3.2 15.0 - - - +
236B GLU* 3.8 6.7 - - - +
237B ALA 3.5 3.4 - - - -
238B GLN* 1.3 95.9 - - + +
240B ILE* 1.3 60.9 + - + +
242B GLU* 3.3 3.1 + - - +
243B LEU* 2.9 29.1 + - - +
277B PHE* 4.0 12.3 - - + -
280B ILE* 3.9 17.8 - - + +
281B ASN* 3.6 21.1 - - - +
284B TYR* 3.6 24.2 - - + -
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 3.7 25.7 - - + +
26B PHE* 3.6 34.1 - - + -
28B LEU* 3.9 27.4 - - + +
29B LEU* 3.9 22.9 - - + -
236B GLU 3.7 18.2 - - - +
237B ALA 3.0 7.2 + - - +
239B PRO* 1.3 83.7 - - + +
241B ILE* 1.3 69.3 + - + +
243B LEU* 3.1 7.8 + - - +
244B ALA* 2.9 21.0 + - - +
277B PHE* 4.5 8.3 - - + -
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.8 2.0 - - + -
145B LEU* 3.7 30.1 - - + -
160B LEU* 3.8 24.8 - - + +
226B VAL* 5.7 0.2 - - + -
227B MET* 5.0 2.0 - - + -
230B ILE* 3.9 20.4 - - + -
233B PHE* 3.3 50.7 - - + -
237B ALA* 2.8 22.8 + - + +
238B GLN 3.8 3.6 - - - +
240B ILE* 1.3 77.4 - - + +
242B GLU* 1.3 61.6 + - - +
244B ALA* 3.4 7.4 + - - +
245B ALA* 3.1 22.7 + - - +
302B FPS 4.4 6.1 - - + -
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B MET* 3.5 30.7 - - - +
230B ILE* 4.8 3.1 - - + +
238B GLN 3.0 14.8 + - - +
239B PRO 3.5 1.8 - - - +
241B ILE* 1.3 75.8 - - - +
243B LEU* 1.3 67.7 + - - +
245B ALA* 3.4 1.0 + - - +
246B ARG* 2.4 65.6 + - - +
280B ILE* 3.4 20.0 - - + +
283B LYS* 2.9 20.7 + - - -
284B TYR* 3.2 31.2 + - - -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.8 17.5 - - + -
25B ALA* 3.9 13.0 - - + -
28B LEU* 3.8 19.3 - - + -
239B PRO 2.9 16.5 + - - +
240B ILE* 3.6 6.3 - - - +
242B GLU* 1.3 78.2 - - - +
244B ALA* 1.3 64.1 + - - +
246B ARG* 3.1 1.0 + - + -
247B ILE* 2.9 43.0 + - + +
273B LYS 3.5 20.9 - - - +
276B LEU* 3.9 12.6 - - + -
277B PHE* 3.7 34.5 - - + +
280B ILE* 3.2 8.7 - - + +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 3.2 42.1 - - + -
25B ALA* 4.2 8.6 - - + +
26B PHE* 4.2 20.4 - - + -
160B LEU* 5.9 1.8 - - + -
164B LEU* 5.1 5.8 - - + -
240B ILE 2.9 12.8 + - - +
241B ILE* 3.5 11.0 - - - +
243B LEU* 1.3 76.5 - - - +
245B ALA* 1.3 62.8 + - - +
247B ILE* 3.5 9.0 + - - +
248B TYR* 3.5 7.6 + - - +
302B FPS 5.8 2.5 - - + -
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LEU* 4.0 20.4 - - + -
164B LEU* 4.3 12.7 - - + +
223B PHE* 3.3 29.1 - - + -
227B MET* 4.0 5.6 - - + -
241B ILE 3.1 14.1 + - - +
242B GLU 3.7 2.5 - - - +
244B ALA* 1.3 78.6 - - - +
246B ARG* 1.3 60.3 + - - +
248B TYR* 3.2 4.7 + - - +
249B ILE* 2.9 29.5 + - - +
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Residues in contact with ARG 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.7 31.8 - - + -
227B MET* 4.5 6.5 - - - +
242B GLU* 2.4 59.6 + - + +
243B LEU* 3.9 4.7 - - - +
245B ALA* 1.3 70.4 - - - +
247B ILE* 1.3 62.0 + - - +
249B ILE* 3.7 12.7 - - - +
250B GLU* 2.9 31.0 + - - +
276B LEU* 4.1 24.5 - - + +
279B GLU* 6.0 1.1 - - - -
280B ILE* 4.4 11.7 - - + +
283B LYS* 3.8 11.3 - - - +
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 3.8 42.6 - - - +
22B PHE* 5.1 0.2 - - + -
24B TYR* 4.8 1.3 - - + -
25B ALA* 4.3 9.9 - - + -
243B LEU* 2.9 43.7 + - + +
244B ALA* 3.5 9.2 - - - +
245B ALA 3.2 0.2 - - - -
246B ARG* 1.3 78.0 - - - +
248B TYR* 1.3 59.3 + - + +
250B GLU* 3.3 5.5 - - - +
251B ILE* 3.1 24.2 + - + +
268B VAL* 3.6 17.1 - - + +
273B LYS* 3.8 27.8 - - + -
276B LEU* 4.1 11.9 - - + -
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Residues in contact with TYR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 3.6 5.6 - - - -
22B PHE* 3.2 34.1 - + - -
164B LEU* 3.1 57.7 - - + -
167B ILE* 3.3 41.3 - - + +
168B ASN* 3.1 31.8 + - + -
171B ARG* 3.8 1.9 + - - -
244B ALA 3.5 2.9 + - - +
245B ALA 3.2 3.4 + - - +
246B ARG 3.1 0.4 - - - -
247B ILE* 1.3 77.6 - - - +
249B ILE* 1.3 65.1 + - - +
250B GLU 3.0 1.8 - - - -
251B ILE* 3.1 34.4 + - + +
252B LEU* 3.5 3.1 + - - +
302B FPS 2.9 31.4 + - + +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 3.8 19.7 - - + -
220B GLU* 4.3 16.8 - - + +
223B PHE* 3.5 50.9 - - + -
245B ALA 2.9 16.8 + - - +
246B ARG* 3.2 12.8 + - - +
248B TYR* 1.3 76.9 - - - +
250B GLU* 1.3 64.3 + - - +
252B LEU* 3.3 31.7 - - + +
253B ASP* 3.7 5.9 + - - +
256B ARG* 5.3 1.0 + - - -
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B ARG 2.9 16.5 + - - +
247B ILE* 3.3 9.9 - - - +
248B TYR 3.0 0.2 - - - -
249B ILE* 1.3 78.8 - - - +
251B ILE* 1.3 65.2 + - - +
252B LEU 3.1 1.6 - - - -
253B ASP* 3.1 22.1 + - - +
254B GLU* 3.0 30.7 + - - +
257B GLN* 5.5 1.4 - - - +
268B VAL* 4.2 22.2 - - + -
272B LYS* 3.9 26.3 + - - -
276B LEU* 4.2 18.8 - - + +
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER* 3.9 12.6 - - - +
167B ILE* 4.4 9.0 - - + +
171B ARG* 3.8 47.1 - - + +
247B ILE* 3.1 15.4 + - + +
248B TYR* 3.1 47.7 + - + +
250B GLU* 1.3 77.8 - - - +
252B LEU* 1.3 64.3 + - + +
254B GLU* 3.0 8.3 + - - +
255B VAL* 3.0 22.9 + - + +
266B VAL* 4.3 4.0 - - + -
267B PHE* 5.1 5.2 - - - -
268B VAL* 3.7 18.6 - - + +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ILE* 4.2 19.1 - - + +
170B LEU* 3.7 33.7 - - + -
212B TRP* 3.7 20.3 - - + -
216B ALA* 4.2 11.4 - - + +
219B ALA* 5.2 0.7 - - + -
220B GLU* 3.7 36.1 - - + +
248B TYR 3.5 8.9 + - - +
249B ILE* 3.3 25.1 + - + +
251B ILE* 1.3 79.7 - - + +
253B ASP* 1.3 59.7 + - - +
255B VAL* 3.2 14.0 + - + +
256B ARG* 3.2 27.5 + - - +
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Residues in contact with ASP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ILE 3.7 3.0 + - - +
250B GLU* 3.1 30.4 + - - +
252B LEU* 1.3 78.4 - - - +
254B GLU* 1.3 66.3 + - - +
256B ARG* 3.2 23.7 + - - +
257B GLN* 3.0 39.9 + - - +
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU* 3.0 28.8 + - - +
251B ILE* 3.0 6.7 + - - +
253B ASP* 1.3 76.6 - - - +
255B VAL* 1.3 63.1 + - - +
257B GLN* 3.6 20.1 + - - +
258B ALA* 3.1 24.8 + - - +
266B VAL* 3.4 26.8 - - + +
267B PHE 4.1 25.7 - - - +
268B VAL* 4.5 10.1 - - + +
272B LYS* 5.3 6.4 - - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU 4.2 4.9 - - - +
171B ARG* 4.1 23.6 - - - +
208B TYR* 6.1 0.2 - - - +
212B TRP* 3.7 30.7 - - + +
251B ILE* 3.0 17.3 + - + +
252B LEU* 3.6 6.5 - - + +
253B ASP 3.1 0.4 - - - -
254B GLU* 1.3 78.8 - - - +
256B ARG* 1.3 57.1 + - - +
258B ALA* 3.2 2.8 + - - +
259B ASN 3.1 4.3 + - - -
260B TYR* 2.7 54.4 + - + -
261B THR* 4.7 3.1 - - + +
266B VAL* 3.7 24.2 - - + -
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B TRP* 3.9 7.5 - - + -
213B GLU* 2.9 35.8 + - - +
216B ALA* 4.0 7.5 - - - +
220B GLU* 2.9 31.9 + - - -
249B ILE 5.3 1.0 + - - -
252B LEU* 3.2 28.0 + - - +
253B ASP* 3.2 28.8 + - - +
255B VAL* 1.3 76.1 - - - +
257B GLN* 1.3 54.5 + - + +
259B ASN* 2.6 28.6 + - - +
260B TYR* 3.6 33.1 - - + +
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Residues in contact with GLN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLU* 5.5 1.4 - - - +
253B ASP* 3.0 31.1 + - - +
254B GLU* 3.8 25.7 - - - +
256B ARG* 1.3 76.3 - - + +
258B ALA* 1.3 57.2 + - - +
259B ASN* 3.1 3.8 + - - +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLU 3.1 18.4 + - - +
255B VAL 3.9 2.7 - - - +
256B ARG 3.1 0.4 - - - -
257B GLN* 1.3 74.6 - - - +
259B ASN* 1.3 69.5 + - - +
260B TYR 3.3 1.3 - - - -
261B THR* 3.3 36.6 + - + +
264B GLU* 5.6 4.3 - - + +
266B VAL* 3.9 12.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il